The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.

New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan. www.biorxiv.org/content/10.1...

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

I’m excited to highlight our latest paper, just published in Cell 🎉 We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression. 1/n 🧪 www.cell.com/cell/fulltex...

Very important work! Congratulations @nvictus.bsky.social and Thomas!

Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab. www.biorxiv.org/content/10.1... 1/

The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...

🧬 @science.org Rules of engagement for condensins and cohesins guide mitotic chromosome formation | Science www.science.org/doi/10.1126/... @edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.

Excited to share our latest work on how cells fold their genomes, and build mitotic chromosomes! Out in Science today! Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes! With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs. See thread below:

Job Dekker, PhD, and colleagues identify simple rules for genome folding during mitosis: direc.to/naBG Rules of engagement for chromosome folding machines define how cells organize genomes. Understanding how cells achieve mitosis may provide insights into genetic mutations. #ScienceSky

Nice work! Go TADs!

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...

Fantastic work! Congratulations!

Important paper showing that acetylation of trans-acting factors rather than histones controls transcriptional bursting dynamics www.cell.com/molecular-ce...

A must read for any (systems) biologist! www.cell.com/cell-systems...

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨ We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation. 📥 Free-download link: authors.elsevier.com/a/1keGn,LqAr...

Excited to share our work on archaeal 3D genome! This paper revealed how an archaeal SMC complex sculpts TAD-like domains by cooperating with a roadblock NAP and physical properties of DNA. Many congrats to our talented PhD student Kodai! www.nature.com/articles/s41...

Go TADs! Very nice and elegant study showing enhancer-promoter connectivity within TADs genesdev.cshlp.org/content/earl...

Fabulous study! Congratulations!

New discovery from our #CDlab reported in Cell @cp-cell.bsky.social today: SMC motor proteins have a left-right ‘gearbox’ and can switch direction in DNA loop extrusion! www.sciencedirect.com/science/arti... 1/

Mandatory curriculum for any graduate student or post-doc 😆 www.youtube.com/shorts/vavfB...

Important independent calibration of Hi-C data: www.biorxiv.org/content/10.1...

How does a TFs function depend on the promoter it regulates? We know that a TF can have different effects on different promoters. For example, consider this case: CpxR regulates ldtCp, yccAp, efeUp at a similar location. Yet two of them are activated, one repressed #GeneReg 🧪 tinyurl.com/3hr9njnd

Here is an amazing study: universal control of RNA pol by transcription factors. Amazing work by Brewster lab!! www.biorxiv.org/content/10.1...

This is a truly groundbreaking study! Cell death after pol2 inhibition is through a regulated death pathway, and not because transcription ceases.

Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it" www.cell.com/action/showP...